Bug#971111: gubbins: FTBFS: pkg_resources.extern.packaging.requirements.InvalidRequirement: Parse error at "'/build/g'": Expected W:(abcd...)
Control: tag -1 patch Hi there, The code path with the odd call to pkg_resources to get the program version seems to have been put there specifically for the case of build time testing. I pushed a small workaround in debian/rules to make sure the "gubbins" executable is part of the PATH at build time testing, so that it can be used as well as pkg_resources specification. The build goes through with this change, as well as autopkgtesting. https://salsa.debian.org/med-team/gubbins/-/commit/e6d7228fdeb320ee10ef1c2dd094d80a807f2c7b The bug is still there somehow, but should not occur during normal operation of the package, as the case is really specific to the build time testing. I hope this helps, Kind Regards, -- Étienne Mollier Old rsa/3072: 5ab1 4edf 63bb ccff 8b54 2fa9 59da 56fe fff3 882d New rsa/4096: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da Sent from /dev/pts/5, please excuse my verbosity.
Bug#971111: gubbins: FTBFS: pkg_resources.extern.packaging.requirements.InvalidRequirement: Parse error at "'/build/g'": Expected W:(abcd...)
Control: tags -1 upstream Control: forewarded -1 https://github.com/sanger-pathogens/gubbins/issues/286 On Fri, Oct 30, 2020 at 02:38:03PM +0500, Andrey Rahmatullin wrote: > python/gubbins/common.py::parse_and_run() constructs an absolute path for > the executable and then passes it to pkg_resources.get_distribution(). I > have no idea what does this code want to achieve, as get_distribution() > takes requirement specifications, not file paths. Thanks for checking - I've forwarded the issue upstream. Kind regards Andreas. -- http://fam-tille.de
Bug#971111: gubbins: FTBFS: pkg_resources.extern.packaging.requirements.InvalidRequirement: Parse error at "'/build/g'": Expected W:(abcd...)
Hi, Aidan Delaney is mentioned inside the debian/control file but this address was bouncing. I'm writing to other copyright holders and will open an issue on Github about the bug https://bugs.debian.org/97 Kind regards Andreas. On Fri, Oct 30, 2020 at 02:38:03PM +0500, Andrey Rahmatullin wrote: > python/gubbins/common.py::parse_and_run() constructs an absolute path for > the executable and then passes it to pkg_resources.get_distribution(). I > have no idea what does this code want to achieve, as get_distribution() > takes requirement specifications, not file paths. > > -- > WBR, wRAR -- http://fam-tille.de
Bug#971111: gubbins: FTBFS: pkg_resources.extern.packaging.requirements.InvalidRequirement: Parse error at "'/build/g'": Expected W:(abcd...)
Control: tags -1 help
Control: forwarded -1 Aidan Delaney
Hi,
I admit I have no idea what might have caused these pkg_resources
related errors and how to fix these.
Any help would be welcome
Andreas.
On Sun, Sep 27, 2020 at 08:45:17PM +0200, Lucas Nussbaum wrote:
> Source: gubbins
> Version: 2.4.1-2
> Severity: serious
> Justification: FTBFS on amd64
> Tags: bullseye sid ftbfs
> Usertags: ftbfs-20200926 ftbfs-bullseye
>
> Hi,
>
> During a rebuild of all packages in sid, your package failed to build
> on amd64.
>
> Relevant part (hopefully):
> > make[3]: Entering directory '/<>'
> > make[3]: Leaving directory '/<>'
> > make[2]: Leaving directory '/<>'
> > cd python && \
> > python3 setup.py test
> > running test
> > WARNING: Testing via this command is deprecated and will be removed in a
> > future version. Users looking for a generic test entry point independent of
> > test runner are encouraged to use tox.
> > running egg_info
> > creating gubbins.egg-info
> > writing gubbins.egg-info/PKG-INFO
> > writing dependency_links to gubbins.egg-info/dependency_links.txt
> > writing entry points to gubbins.egg-info/entry_points.txt
> > writing requirements to gubbins.egg-info/requires.txt
> > writing top-level names to gubbins.egg-info/top_level.txt
> > writing manifest file 'gubbins.egg-info/SOURCES.txt'
> > reading manifest file 'gubbins.egg-info/SOURCES.txt'
> > writing manifest file 'gubbins.egg-info/SOURCES.txt'
> > running build_ext
> > /<>/python/gubbins/common.py:538: DeprecationWarning: invalid
> > escape sequence \d
> > elif re.match('^\d', vcf_line) is not None:
> > /<>/python/gubbins/common.py:613: DeprecationWarning: invalid
> > escape sequence \d
> > search_obj = re.search('misc_feature([\d]+)..([\d]+)$', line)
> > /<>/python/gubbins/common.py:620: DeprecationWarning: invalid
> > escape sequence \=
> > search_taxa = re.search('taxa\=\"([^"]+)\"', line)
> > /usr/lib/python3/dist-packages/dendropy/utility/container.py:357:
> > DeprecationWarning: Using or importing the ABCs from 'collections' instead
> > of from 'collections.abc' is deprecated since Python 3.3, and in 3.9 it
> > will stop working
> > class CaseInsensitiveDict(collections.MutableMapping):
> > test_concatenate_fasta_files
> > (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods) ... ok
> > test_get_sequence_names_from_alignment
> > (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods) ... ok
> > test_number_of_sequences_in_alignment
> > (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods) ... ok
> > test_reconvert_fasta_file
> > (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods) ... ok
> > test_reinsert_gaps_into_fasta_file
> > (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods) ... ok
> > test_get_recombination_files
> > (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations)
> > ... ok
> > test_multiple_files_have_one_match
> > (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations)
> > ... ok
> > test_reading_embl_file
> > (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations)
> > ... ok
> > test_two_files_are_different
> > (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations)
> > ... ok
> > test_two_files_are_same
> > (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations)
> > ... ok
> > test_cleanup (gubbins.tests.test_dependencies.TestExternalDependencies) ...
> > ERROR
> > test_fasttree (gubbins.tests.test_dependencies.TestExternalDependencies)
> > ... ERROR
> > test_hybrid (gubbins.tests.test_dependencies.TestExternalDependencies) ...
> > ERROR
> > test_iqtree (gubbins.tests.test_dependencies.TestExternalDependencies) ...
> > ERROR
> > test_raxml (gubbins.tests.test_dependencies.TestExternalDependencies) ...
> > ERROR
> > test_rename_final_output
> > (gubbins.tests.test_dependencies.TestExternalDependencies) ... ERROR
> > test_dont_filter_input_file_with_multiple_duplicate_sequences
> > (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta) ... ok
> > test_filter_out_alignments_with_too_much_missing_data
> > (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta) ... ok
> > test_input_file_with_all_duplicate_sequences
> > (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta) ... ok
> > test_input_file_with_multiple_duplicate_sequences
> > (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta) ... ok
> > test_input_file_with_no_duplicate_sequences
> > (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta) ... ok
> > test_input_file_with_one_duplicate_sequences
> > (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta) ... ok
> > test_filter_out_removed_taxa_from_tree
> > (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok
> > test_has_tree_been_seen_before
> > (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok
> >
Bug#971111: gubbins: FTBFS: pkg_resources.extern.packaging.requirements.InvalidRequirement: Parse error at "'/build/g'": Expected W:(abcd...)
python/gubbins/common.py::parse_and_run() constructs an absolute path for the executable and then passes it to pkg_resources.get_distribution(). I have no idea what does this code want to achieve, as get_distribution() takes requirement specifications, not file paths. -- WBR, wRAR signature.asc Description: PGP signature
Bug#971111: gubbins: FTBFS: pkg_resources.extern.packaging.requirements.InvalidRequirement: Parse error at "'/build/g'": Expected W:(abcd...)
Source: gubbins
Version: 2.4.1-2
Severity: serious
Justification: FTBFS on amd64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20200926 ftbfs-bullseye
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> make[3]: Entering directory '/<>'
> make[3]: Leaving directory '/<>'
> make[2]: Leaving directory '/<>'
> cd python && \
> python3 setup.py test
> running test
> WARNING: Testing via this command is deprecated and will be removed in a
> future version. Users looking for a generic test entry point independent of
> test runner are encouraged to use tox.
> running egg_info
> creating gubbins.egg-info
> writing gubbins.egg-info/PKG-INFO
> writing dependency_links to gubbins.egg-info/dependency_links.txt
> writing entry points to gubbins.egg-info/entry_points.txt
> writing requirements to gubbins.egg-info/requires.txt
> writing top-level names to gubbins.egg-info/top_level.txt
> writing manifest file 'gubbins.egg-info/SOURCES.txt'
> reading manifest file 'gubbins.egg-info/SOURCES.txt'
> writing manifest file 'gubbins.egg-info/SOURCES.txt'
> running build_ext
> /<>/python/gubbins/common.py:538: DeprecationWarning: invalid
> escape sequence \d
> elif re.match('^\d', vcf_line) is not None:
> /<>/python/gubbins/common.py:613: DeprecationWarning: invalid
> escape sequence \d
> search_obj = re.search('misc_feature([\d]+)..([\d]+)$', line)
> /<>/python/gubbins/common.py:620: DeprecationWarning: invalid
> escape sequence \=
> search_taxa = re.search('taxa\=\"([^"]+)\"', line)
> /usr/lib/python3/dist-packages/dendropy/utility/container.py:357:
> DeprecationWarning: Using or importing the ABCs from 'collections' instead of
> from 'collections.abc' is deprecated since Python 3.3, and in 3.9 it will
> stop working
> class CaseInsensitiveDict(collections.MutableMapping):
> test_concatenate_fasta_files
> (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods) ... ok
> test_get_sequence_names_from_alignment
> (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods) ... ok
> test_number_of_sequences_in_alignment
> (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods) ... ok
> test_reconvert_fasta_file
> (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods) ... ok
> test_reinsert_gaps_into_fasta_file
> (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods) ... ok
> test_get_recombination_files
> (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations)
> ... ok
> test_multiple_files_have_one_match
> (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations)
> ... ok
> test_reading_embl_file
> (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations)
> ... ok
> test_two_files_are_different
> (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations)
> ... ok
> test_two_files_are_same
> (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations)
> ... ok
> test_cleanup (gubbins.tests.test_dependencies.TestExternalDependencies) ...
> ERROR
> test_fasttree (gubbins.tests.test_dependencies.TestExternalDependencies) ...
> ERROR
> test_hybrid (gubbins.tests.test_dependencies.TestExternalDependencies) ...
> ERROR
> test_iqtree (gubbins.tests.test_dependencies.TestExternalDependencies) ...
> ERROR
> test_raxml (gubbins.tests.test_dependencies.TestExternalDependencies) ...
> ERROR
> test_rename_final_output
> (gubbins.tests.test_dependencies.TestExternalDependencies) ... ERROR
> test_dont_filter_input_file_with_multiple_duplicate_sequences
> (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta) ... ok
> test_filter_out_alignments_with_too_much_missing_data
> (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta) ... ok
> test_input_file_with_all_duplicate_sequences
> (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta) ... ok
> test_input_file_with_multiple_duplicate_sequences
> (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta) ... ok
> test_input_file_with_no_duplicate_sequences
> (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta) ... ok
> test_input_file_with_one_duplicate_sequences
> (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta) ... ok
> test_filter_out_removed_taxa_from_tree
> (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok
> test_has_tree_been_seen_before
> (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok
> test_internal_node_taxons_removed_when_used_as_starting_tree
> (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok
> test_remove_internal_node_labels
> (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok
> test_reroot_tree (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok
> test_reroot_tree_at_midpoint
> (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok
> test_reroot_tree_with_outgroup
> (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok
> test_reroot_tree_with_outgroups
>
